Cool applications for Linux

http://linuxondesktop.blogspot.com/2007/07/35-cool-applications-to-install-on.html

Great website, I highly recommend it.

HP scanjet 4370 on Gutsy Gibbon (Ubuntu 7.10)

Here's how I got our scanner working on Gutsy.

Install sane:

sudo aptitude install sane sane-utils

Then find out where your scanner resides:

sane-find-scanner

You're interested in the series of usb ports that your usb is connected to:

found USB scanner (vendor=0x03f0 [hewlett packard],
product=0x4105 [hp scanjet], chip=rts8822L-01H?) at libusb:007:006

In my case, the scanner is plugged into usb port 007 and subport 006 (I have no idea if that's the proper way to talk about it, but you'll see that it will work to think like that)
Then, you need the driver for your scanner, so go to the sane supported devices page and find your scanner. You access the driver by clicking under the 'Backend' link.
At least in theory, this driver is supposed to be in the sane-backends distribution. I'm not sure where to get it (already come with sane?). Anyway, my device wasn't really recognized when firing up 'xsane' until I downloaded and installed the driver.
Now, we have to set the permissions such that we can access our scanner. Notice that we use the the usb port information gleaned about to accomplish this:

sudo chmod a+rw /proc/bus/usb/007/006

A person is supposed to be able to automate that process, but I haven't figured it out yet. In any case, we can now fire up sane with the command 'xsane' or install 'gimp2.0-quiteinsane' to access from within gimp.

Using LCD Projectors or monitors with Ubuntu Gutsy Gibbon and Nvidia

Under Edgy and Feisty, you could just restart your machine, hit your [CRT/LCD] (Fn+F8 on my machine) while it was loading and it would automatically do this for you.

Under Gutsy, this will work (may be easier/better ways to do this):

1. run command 'nvidia-settings' and go to 'X Server Display Configuration'
   
2. If you are all plugged in, there should be two grey boxes displayed, one labeled 'LGP' (your LCD screen) and another (mine's labeled 'LG').
   
3. Change the resolution of your current display to match what you will be using (most projectors are 1024x768)
   
4. Now, click on the LG box. (The way to control which display you are dealing with are clicking and moving those boxes)
   
5. You should see a box with a Configuration: Disabled and button [Configure]; click the Configure button.
   
6. How Should this display device be configured? Click 'TwinView'
   
7. Resolution 'Auto'
   
8. Position 'Clones'
   
9. Then hit 'Apply'
   

That's it!

If you want to run this configuration with no setup, then click on the 'Save to X Configuration File' and copy it over your /etc/X11/xorg.conf file whenever you need it (make sure you backup your original xorg.conf file!)

To undo it, click on the Configure button for LG, and click 'Disabled'. Then, change the resolution for your current screen and hit the 'Apply' button.

NOTE: this does not want to work under wmii-ruby because it does not want to respond to the change in resolution from gnome-display-properties.

Gutsy Gibbon broken matplotlib, pylab

Usually, Ubuntu's package management system gets everything right. However, on Gutsy Gibbon when you install the very handy matplotlib it gives you a broken installation. Basically, you'll get some error messages like this:

>>> import pylab
Traceback (most recent call last):
  File "", line 1, in ?
  File "/usr/lib/python2.4/site-packages/pylab.py", line 1, in ?
    from matplotlib.pylab import *
  File "/usr/lib/python2.4/site-packages/matplotlib/pylab.py", line 199, in ?
    import cm
  File "/usr/lib/python2.4/site-packages/matplotlib/cm.py", line 5, in ?
    import colors
  File "/usr/lib/python2.4/site-packages/matplotlib/colors.py", line 38, in ?
    from numerix import array, arange, take, put, Float, Int, putmask, \
  File "/usr/lib/python2.4/site-packages/matplotlib/numerix/__init__.py", line 82, in ?
    import numpy
  File "/usr/lib/python2.4/site-packages/numpy/__init__.py", line 43, in ?
    import linalg
  File "/usr/lib/python2.4/site-packages/numpy/linalg/__init__.py", line 4, in ?
    from linalg import *
  File "/usr/lib/python2.4/site-packages/numpy/linalg/linalg.py", line 25, in ?
    from numpy.linalg import lapack_lite
ImportError: /usr/lib/atlas/liblapack.so.3: undefined symbol: ATL_chemv

So, I think they are trying to allow you to use whatever linear algebra backend you want. A fix (maybe there are better ones) is to install lapack3:

 sudo aptitude install lapack3

CSS for ruby syntax highlighting

Add this to your css to get ruby code colored nicely.

from http://redcorundum.blogspot.com/2006/07/syntax-coloring.html

pre.code {
  padding: 1ex 1ex 1ex 1ex;
  border: 4px groove #CC0000;
  overflow-x: auto;
}

pre.code span.attribute { color: #009900; }
pre.code span.char { color: #F00; }
pre.code span.class { color: #A020F0; font-weight: bold; }
pre.code span.comment { color: #0000FF; }
pre.code span.constant { color: #008B8B; }
pre.code span.escape { color: #6A5ACD; }
pre.code span.expr { color: #2222CC; }
pre.code span.global { color: #11AA44; }
pre.code span.ident { color: #000000; }
pre.code span.keyword { color: #A52A2A; font-weight: bold; }
pre.code span.method { color: #008B8B; }
pre.code span.module { color: #A020F0; font-weight: bold; }
pre.code span.number { color: #DD00DD; }
pre.code span.punct { color: #6A5ACD; }
pre.code span.regex { color: #DD00DD; }
pre.code span.string { color: #DD00DD; }
pre.code span.symbol { color: #008B8B; }

Install Ubuntu as a file in windows with one-click

If you want to try out linux (Ubuntu), this is BY FAR the easiest method. Just download this installer. The next time you reboot you can choose Windows or Linux:

http://wubi-installer.org/index.php

Basically, a file (6GB by default) is allocated inside of windows and a boot loader is installed. On reboot, you can choose windows or linux. When you are done, you can uninstall it and it goes away. Or, there are ways to migrate that file into a fresh partition if you want.

Very smooth.

R help in a browser

Really annoying to try to look up docs in a window you are using. Instead, try this:

help.start()  # this will start up documentation in a browser
help(plot)    # shows documentation in browswer window now!

data.frame in R (the key object)

I've been wading through R trying to figure out how it all works. It looks like the most important data structure is the data frame, and here I demo how to make a dataframe that a person can then play with. Yes, you can import data from a spreadsheet, but a person should understand the underlying data structure.

A data.frame is just a list of vectors or matrices where each has the same number of rows (think of the vectors as columns). It really is just the same as data in a spreadsheet:

var1	var2	var3	fac1	fac2
1	3	4	hot	TX
0	2	3	cold	WI
3	8	2	cold	UT

In fact, when one reads in this type of info, one gets a data.frame back:

df = read.csv(".csv", quote="")  # <-reads an unquoted csv file with headers

So, assuming we have some data like the above, now lets make it in R:

> var1 <- c(1,0,3)    #  '<-' is the assignment operator (like a directional '=')
                      #  'c()' is the concatenate operator (makes lists of things)
> var2 <- c(3,2,8)
> var3 <- array( c(4,3,2), c(3) )  # here's how you make a more mathematical vector

> fac1 <- c("hot", "cold", "cold")
> fac2 <- c("TX","WI","UT")

# alright, lets add all this stuff together into a dataframe:

> df <- data.frame(var1,var2,var3,fac1,fac2, row.names=NULL, check.rows=TRUE)

# creates this:
  var1 var2 var3 fac1 fac2
1    1    3    4  hot   TX
2    0    2    3 cold   WI
3    3    8    2 cold   UT

# want to see the names of the columns in the dataset:
> names(df)
[1] "var1" "var2" "var3" "fac1" "fac2"

# change the names:
> names(df) <- c("height", "weight", "nose.length", "temp", "state")
> df
  height weight nose.length temp state
1      1      3           4  hot    TX
2      0      2           3 cold    WI
3      3      8           2 cold    UT

# so, now we have a data.frame, the preferred data structure in R.  Let the magic begin:

> plot(df)  

Installing and basic plotting in R

Windows users:
http://cran.r-project.org/bin/windows/base/
Download R-2.6.1-win32.exe and install it like any program.
Start it like any other program from the start menu

Linux users:
sudo apt-get install r-base
Just type R in the terminal

Read in a file
Go into excel or even a text editor and create a simple data set like this:
1,3
2,5
2,6
3,8
4,4
6,3
7,9
Where the second column is after the comma.
Save your file as a .csv
Look up where you saved it and insert that as the location in the following code:
data<-read.table("/home/eldon/Desktop/data.csv",sep=",") #this reads in your data and assigns it to the data frame "data"
plot(data) #this gives you a simple plot of your data
If you want to learn more about simple plotting just enter:
help(plot)

Scientists for Better PCR

http://bio-rad.cnpg.com/lsca/videos/ScientistsForBetterPCR/

Good for a laugh

What about R?

Isn't R important enough to put into the subtitle?

R from ruby

rsruby lets you run supposedly any function in R from ruby.

Elaborating on the sci-ruby page

sudo apt-get install r-base ruby1.9.1-full ruby1.9.1-dev
sudo ln -s /usr/lib/R/lib/libR.so /usr/lib/libR.so
sudo ln -s /usr/share/R/include/R.h /usr/include/R.h
gem install rsruby -- --with-R-dir=/usr/share/R

I thought this was necessary, but don't so much any more:

# add a line to your .bashrc file to point to R:
echo "export R_HOME=/usr/lib/R" >> ~/.bashrc
source ~/.bashrc   # read the bashrc file to get the variable